This chapter delves into the multifaceted aspects of sustainability within the biofuel supply chain, aiming to assess its overall value. The significance of sustainability dimensions in generating value has been widely acknowledged. Employing an appropriate framework of key performance indicators ensures precise valuation of the chain. Initially, the chapter outlines the relevance and advantages of biofuels, followed by an exploration of their various types. A novel approach is introduced by conceptualizing an energy chain model that integrates sustainability dimensions and metrics. Uncertainty, particularly of the rough type, is a critical factor in this analysis. Rough set theory stands out as an effective mathematical method for addressing such uncertainties. Subsequently, the rough linear mathematical programming model is optimized using advanced tools, yielding the sustainable value of the chain.